Structures and Vibrational Frequencies of Molecular Clusters


Principal Investigator

Gad Fischer

Department of Chemistry

Faculty of Science


Xiaolin Cao

Fiona Bettens

Department of Chemistry

Faculty of Science

John P. Maier

Institute for Physical Chemistry

Basel University


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This project has been approached from a number of angles, and the work has been expanded from the
original study of halocarbon clusters. The structures and vibrational frequencies of long chain hydrocarbon molecules (acetylene clusters) have allowed comparison with molecules believed to exist in interstellar space. The amino acids in solution and in the solid state do not exist as isolated molecules but in ionized clusters. Molecular structure and frequency calculations have been carried out for a model in which the isolated but ionized amino acid molecules sit within a solvation shell (cluster) of KBr molecules. The computed results have been compared with the vibrational spectrum measured using a new experimental technique. This work leads to a better understanding of the structure and behaviour of the amino acids.


What are the results to date and the future of the work?

Ground state calculations of the optimized geometries and vibrational frequencies of the poly acetylenes, HCnH n=3-15, and the isoelectronic ions HCn-, have been variously carried out at HF/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p) and CASSCF/6-31G(d) levels, both with and without the constraint of linearity. Excited state calculations at the CIS/6-31G(d) and CASSCF/6-31G* levels have focussed mainly on the intense 1A1 excited states. Calibration of the CIS results has been achieved by comparison with the differences between the similarly calculated excited state energies, and experimentally measured transitions for the polyacetylenes. Despite the calibration, discrepancies of about 0.9 eV remain with the energies for the HCn-series measured by the Maier group. CASSCF calculations for the smaller members of these families of molecules are currently being undertaken to provide a check on the consistency of the CIS results. Future work will involve extending the CASSCF calculations to longer chains.

An innovative infrared sampling technique has been developed to obtain more informative infrared spectra of amino acids and nucleic acid bases. The technique is a room-temperature version of the matrix isolation method. It involves the spraying of a solution of sample and matrix molecules onto an infrared window. In the current work the solvent has been restricted to water and the matrix to KBr. Mono-molecular spectra of these samples have not been

- Appendix A



previously obtained. The method also allows measurement of the zwitterionic form of the amino acids, and different tautomers of the nucleic acid bases. Vibrational frequencies calculated by ab initio methods involving a solvated molecule have provided good agreement with frequencies measured in spectra recorded using the new spray technique. Future work will involve extension of the measurements and calculations to larger amino acids and peptides, and to the formation of dimers of the amino acids, the nucleic acid bases, and to cross dimers.

What computational techniques are used?

GAUSSIAN packages such as HF, HF/SCRF and DFT/SCRF have been used for the amino acid work, and in addition MOLPRO for the HCn- work.


X. Cao and G. Fischer, New Infrared Spectra and the Tautomeric Study of Purine and aL-Alanine with an Innovative Sampling Technique. Spectrochimica Acta A (1999), In press.

Appendix A -